leonarski_fandClaude Opus 5
2e8040c60c
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--model called gemmi::read_pdb unconditionally, so a coordinate file in mmCIF - which is how the PDB serves coordinates by default - was refused outright: Model validation: cannot read model 6G8A.cif: Incorrect file format (perhaps it is cif not pdb?) Worse than the refusal was what followed it. ValidateAgainstModel logged, returned an empty result, and the run went on to finish with exit code 0, no R-free, no maps and nothing in the report - indistinguishable from a run that was never given --model at all. A script that passed a .cif, checked the exit code and grepped for R-free simply got nothing back. Both read sites now go through read_structure_gz with CoorFormat::Detect, so PDB, mmCIF and mmJSON are all read, gzipped or not, and the format comes from the file's content rather than from its name. Detect is passed explicitly: GEMMI otherwise takes the extension and only falls back to the content when it does not recognise one, and a model arrives named however whoever produced it named it. That needed a part of GEMMI the vendored subset had trimmed away. mmread.hpp was already here but its CIF parser was not, so this restores what upstream GEMMI ships: read_cif/mmcif/json/mmread_gz, plus GEMMI's own copies of PEGTL (MIT, Colin Hirsch and Daniel Frey; 155 headers, 672 kB) and sajson (MIT, Chad Austin; one header). Both are listed in THIRD_PARTY_NOTICES.md with their own licence texts, PEGTL's collected by COLLECT.sh and sajson's kept by hand, its terms being a comment block rather than a file. json.cpp carries a one-line change: upstream keeps sajson at the root of its repository, outside the include tree this subset copies, so the include points at where the other bundled headers live. ModelValidationResult gains failure_reason, and a model that was asked for and could not be used now reaches the results report as WARNING: Model validation did not run: model bogus.pdb has no atoms or no unit cell in --mode mx and --mode scale alike. The run still succeeds - a merge that is good is not made bad by a model that was not - but it no longer does so quietly. One log line was making a claim it could not support: the indexing-ambiguity message said the ambiguity was "resolved against the supplied model" while being printed before the model is read, so it announced a resolution that a failed model never performed. It now says the model will be used; the reference branch, where the work really has already happened, keeps the past tense. Verified on the rotation test dataset with a deposited mmCIF, the same file gzipped, an mmCIF under a .pdb name, a PDB, and an unreadable file. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_016WmryXe8ASbNi632sUMfsa
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Third-party software notices
Jungfraujoch is licensed under GPL-3.0 (see LICENSE); the FPGA design is
licensed under CERN-OHL-S-2.0 (see fpga/LICENSE). It builds on a number of
third-party components, acknowledged below as required by their licenses.
This file is the human-readable manifest. The verbatim license texts live in the
licenses/ directory (regenerate with bash licenses/COLLECT.sh). The frontend's
bundled JavaScript dependencies are listed separately in
frontend/dist/THIRD_PARTY_LICENSES.txt, generated at build time (npm run licenses).
All licenses below are GPL-3.0-compatible.
Fetched at build time and statically linked into the C++ binaries
These are downloaded by CMake (FetchContent / ExternalProject) during the first configure and
linked into the Jungfraujoch executables.
| Component | Version | Copyright | License (SPDX) | License text |
|---|---|---|---|---|
| spdlog | 1.17.0 | Gabi Melman | MIT | spdlog.txt |
| Zstandard | (pinned) | Meta Platforms, Inc. | BSD-3-Clause | zstd.txt |
| HDF5 | 2.1.0 | The HDF Group; UIUC | BSD-3-Clause-style | hdf5.txt |
| slsDetectorPackage | 8.0.2 / 9.2.0 | PSI | LGPL-3.0-or-later | LGPL, GPL |
| cpp-httplib | 0.39.0 | Yuji Hirose | MIT | cpp-httplib.txt |
| libzmq (ZeroMQ) | 4.3.5 | iMatix and contributors | MPL-2.0 | libzmq.txt |
| libtiff | 4.7.1 | Sam Leffler; SGI | libtiff (BSD-like) | libtiff.txt |
| FFTW | 3.3.10 | Matteo Frigo; MIT | GPL-2.0-or-later | fftw.txt |
| Ceres Solver | (pinned) | Google Inc. and contributors | BSD-3-Clause | ceres-solver.txt |
| fast-feedback-indexer | (pinned) | PSI | BSD-3-Clause | fast-feedback-indexer.txt |
| libjpeg-turbo | (pinned) | D. R. Commander and others; IJG | IJG + BSD-3-Clause + Zlib | libjpeg-turbo.txt |
| Catch2 | 3.13.0 | Catch2 Authors | BSL-1.0 | catch2.txt |
Catch2 is used only to build the test binary (jfjoch_test) and is not part of any shipped
artifact; it is listed here for completeness.
Vendored directly in the repository
These are copied into the source tree (see the path) rather than fetched.
| Component | Path | Copyright | License (SPDX) | License text |
|---|---|---|---|---|
| nlohmann/json | include/nlohmann/ |
Niels Lohmann | MIT | nlohmann-json.txt |
| Macaron Base64 | include/base64/ |
tomykaira | MIT | base64-macaron.txt |
| TinyCBOR | frame_serialize/tinycbor/ |
Intel Corporation | MIT | tinycbor.txt |
| Bitshuffle | compression/bitshuffle/ |
Kiyoshi Masui | MIT | bitshuffle.txt |
| Bitshuffle (h-perf) | compression/bitshuffle_hperf/ |
Kal Cutter (DECTRIS) | Apache-2.0 | bitshuffle-hperf.txt |
| LZ4 | compression/lz4/ |
Yann Collet | BSD-2-Clause | lz4.txt |
| HLS arbitrary-precision types | fpga/include/ |
Xilinx, Inc. | Apache-2.0 | xilinx-hls-headers.txt |
| GEMMI | gemmi_gph/ |
Global Phasing Ltd. | MPL-2.0 | gemmi.txt |
| PEGTL | gemmi_gph/gemmi/third_party/tao/ |
Dr. Colin Hirsch and Daniel Frey | MIT | pegtl.txt |
| sajson | gemmi_gph/gemmi/third_party/sajson.h |
Chad Austin | MIT | sajson.txt |
| traccc (ACTS) | image_analysis/spot_finding/StrongPixelSet.cpp, SpotExtractorGPU.cu |
CERN, for the benefit of the ACTS project | MPL-2.0 | traccc.txt |
| xbflash.qspi | tools/xbflash.qspi/ |
Xilinx / AMD | Apache-2.0 | xbflash-qspi.txt |
| wingetopt | tools/wingetopt/ |
Todd C. Miller; The NetBSD Foundation | ISC AND BSD-2-Clause | wingetopt.txt |
Runtime libraries and SDKs (shipped in binaries, not in the source tree)
| Component | Used by | License | Notice |
|---|---|---|---|
| Qt 6 | jfjoch_viewer |
LGPL-3.0 | notice, LGPL-3.0 |
| NVIDIA CUDA Toolkit (cudart, cuFFT) | CUDA builds | NVIDIA CUDA EULA | notice, EULA |
| zlib | everywhere (compression) | Zlib | zlib.txt |
| Eigen | analysis libs, Ceres, ffbidx (header-only) | MPL-2.0 (+ BSD parts) | eigen.txt, README |
Frontend (npm) dependencies
The React/TypeScript frontend (frontend/) bundles a large transitive tree of npm packages,
overwhelmingly MIT/ISC/BSD/Apache-2.0 licensed. Their full notices are generated automatically:
cd frontend && npm run licenses # writes dist/THIRD_PARTY_LICENSES.txt
The generated file is produced as part of the frontend build target and installed alongside the
served frontend, so the shipped web UI carries its own attribution.
Notes on weak-copyleft and attribution-sensitive components
- MPL-2.0 (Eigen, GEMMI, libzmq, traccc): file-level copyleft. GEMMI is vendored in
gemmi_gph/in trimmed form; libzmq is fetched at build time; Eigen is provided externally (header-only). The corresponding source is available from each project upstream. - traccc is the one entry that is not a vendored directory. Its sparse connected-component
labelling enters two otherwise first-party files:
StrongPixelSet.cppadapts the SparseCCL source, andSpotExtractorGPU.cufollows the design of its GPU counterpart. MPL-2.0 is file-level, so both files name the origin at the top and are covered bylicenses/traccc.txt. See ACKNOWLEDGEMENT.md for the citation. - FFTW is GPL-2.0-or-later — compatible with, and absorbed by, this project's GPL-3.0 license.
- Apache-2.0 components: where upstream ships a
NOTICEfile, it is reproduced in the correspondinglicenses/text. - Qt (LGPL-3.0) and NVIDIA CUDA (EULA) carry redistribution conditions beyond a copyright
notice; see their dedicated notice files. The verbatim LGPL-3.0 and CUDA EULA texts are bundled
(
licenses/Qt6-LGPL-3.0.txt,licenses/NVIDIA-CUDA-EULA.txt); the CUDA EULA is the one shipped with CUDA Toolkit 12.8 — replace it if you build against a different toolkit version.